Hey Meli...
   Did John Deere put bolts in those rear axle holes from the factory?
If so, were they square head or hex?
   The rowcrop tractors came with about a dozen 5/8" x 2-1/4" studs in those holes. All of the studs had "special hex nuts" on them. The nuts are hex-shaped, but they are about 1-1/2" tall, and rounded on the top. (See below) The nuts would protect you from constantly scraping yourself on the studs as you worked around the tractor. The nuts and studs are used for attaching implements, parts of implements, and brackets for implements to the axles.

The John Deere rear axle
Special Hex nut for rear axle     Part number 30 is a threaded stud. Part number 29 is the long "special hex nut" that served to protect the threads on the stud from rust when nothing was attached to it. Many times, over the years, the studs became rusted to the nuts and came off along with them. That might be why all you have left are the HOLES.

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